Polymerization of nontemplate bases before transcription initiation at the3 ' ends of templates by an RNA-dependent RNA polymerase: An activity involved in 3 ' end repair of viral RNAs

The 3' ends of RNAs associated with turnip crinkle virus (TCV), including s ubviral satellite (sat)C, terminate with the motif CCUGCCC-3'. Transcripts of satC with a deletion of the motif are repaired to wild type (wt) in vivo by RNA-dependent RNA polymerase (RdRp)-mediated extension of abortively sy nthesized oligoribonucleotide primers complementary to the 3' end of the TC V genomic RNA. Repair of shorter deletions, however, are repaired by other mechanisms. SatC transcripts with the 3' terminal CCC replaced by eight non viral bases were repaired in plants by homologous recombination between the similar 3' ends of satC and TCV. Transcripts with deletions of four or fiv e 3' terminal bases, in the presence or absence of nonviral bases, generate d progeny with a mixture of wt and non-wt 3' ends in vivo. In vitro, RdRp-c ontaining extracts were able to polymerize nucleotides in a template-indepe ndent fashion before using these primers to initiate transcription at or ne ar the 3' end of truncated satC templates. The nontemplate additions at the 5' ends of the nascent complementary strands were not random, with a prefe rence for consecutive identical nucleotides. The RdRp was also able to init iate transcription opposite cytidylate, uridylate, guanylate, and possibly adenylate residues without exhibiting an obvious preference. flexibility pr eviously unreported for viral RdRp. The unexpected existence of three diffe rent repair mechanisms for TCV suggests that 3' end reconstruction is criti cal to virus survival.